data_PYL
#
_chem_comp.id PYL
_chem_comp.name PYRROLYSINE
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C12 H21 N3 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-02-07
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 255.313
_chem_comp.one_letter_code O
_chem_comp.three_letter_code PYL
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
PYL CB2 CB2 C 0 1 N N N N N N 3.704 72.211 1.136 3.980 2.442 -0.324 CB2 PYL 1
PYL CG2 CG2 C 0 1 N N R N N N 4.671 71.449 2.044 4.412 1.125 0.325 CG2 PYL 2
PYL CD2 CD2 C 0 1 N N N N N N 3.984 70.864 3.276 5.952 0.975 0.313 CD2 PYL 3
PYL CE2 CE2 C 0 1 N N N N N N 5.175 70.696 4.223 6.169 -0.493 0.022 CE2 PYL 4
PYL N2 N2 N 0 1 N N N N N N 6.149 71.534 3.873 5.110 -1.035 -0.430 N2 PYL 5
PYL CA2 CA2 C 0 1 N N R N N N 5.739 72.323 2.701 3.995 -0.087 -0.540 CA2 PYL 6
PYL C2 C2 C 0 1 N N N N N N 6.927 72.567 1.767 2.729 -0.703 -0.004 C2 PYL 7
PYL O2 O2 O 0 1 N N N N N N 6.764 72.855 0.582 2.784 -1.700 0.685 O2 PYL 8
PYL NZ NZ N 0 1 N N N N N N 8.114 72.417 2.351 1.535 -0.146 -0.288 NZ PYL 9
PYL CE CE C 0 1 N N N N N N 9.389 72.611 1.647 0.304 -0.745 0.234 CE PYL 10
PYL CD CD C 0 1 N N N N N N 10.162 73.741 2.330 -0.900 0.075 -0.233 CD PYL 11
PYL CG CG C 0 1 N N N N N N 9.403 75.065 2.218 -2.185 -0.550 0.312 CG PYL 12
PYL CB CB C 0 1 N N N N N N 10.049 76.170 3.058 -3.389 0.270 -0.155 CB PYL 13
PYL CA CA C 0 1 N N S Y N N 9.934 75.876 4.556 -4.675 -0.355 0.390 CA PYL 14
PYL C C C 0 1 N N N Y N Y 10.671 76.956 5.350 -5.849 0.520 0.034 C PYL 15
PYL OXT OXT O 0 1 N Y N Y N Y 11.889 76.767 5.558 -6.114 1.616 0.762 OXT PYL 16
PYL O O O 0 1 N N N Y N Y 9.999 77.938 5.732 -6.552 0.234 -0.906 O PYL 17
PYL N N N 0 1 N N N Y Y N 8.521 75.845 4.961 -4.860 -1.687 -0.201 N PYL 18
PYL HXT HXT H 0 1 N Y N Y N Y 12.241 77.493 6.060 -6.878 2.146 0.495 HXT PYL 19
PYL HA HA H 0 1 N N N Y N N 10.400 74.901 4.764 -4.604 -0.445 1.474 HA PYL 20
PYL H H H 0 1 N N N Y Y N 8.459 75.652 5.940 -5.668 -2.148 0.192 H PYL 21
PYL H2 HN2 H 0 1 N Y N Y Y N 8.100 76.731 4.768 -4.929 -1.631 -1.206 H2 PYL 22
PYL HB3 HB3 H 0 1 N N N N N N 11.113 76.247 2.790 -3.298 1.292 0.214 HB3 PYL 23
PYL HB2 HB2 H 0 1 N N N N N N 9.546 77.124 2.841 -3.423 0.279 -1.244 HB2 PYL 24
PYL HG3 HG3 H 0 1 N N N N N N 9.393 75.380 1.164 -2.277 -1.572 -0.057 HG3 PYL 25
PYL HG2 HG2 H 0 1 N N N N N N 8.370 74.913 2.565 -2.152 -0.558 1.401 HG2 PYL 26
PYL HD3 HD3 H 0 1 N N N N N N 10.299 73.493 3.393 -0.808 1.097 0.135 HD3 PYL 27
PYL HD2 HD2 H 0 1 N N N N N N 11.145 73.847 1.849 -0.933 0.084 -1.323 HD2 PYL 28
PYL HE3 HE3 H 0 1 N N N N N N 9.978 71.683 1.687 0.213 -1.767 -0.135 HE3 PYL 29
PYL HE2 HE2 H 0 1 N N N N N N 9.195 72.877 0.597 0.338 -0.753 1.323 HE2 PYL 30
PYL HZ HZ H 0 1 N N N N N N 8.139 72.159 3.317 1.491 0.651 -0.839 HZ PYL 31
PYL HA2 HA2 H 0 1 N N N N N N 5.301 73.283 3.010 3.859 0.218 -1.578 HA2 PYL 32
PYL HE22 HE22 H 0 0 N N N N N N 5.219 70.003 5.050 7.102 -1.015 0.178 HE22 PYL 33
PYL HD32 HD32 H 0 0 N N N N N N 3.235 71.556 3.688 6.391 1.590 -0.473 HD32 PYL 34
PYL HD22 HD22 H 0 0 N N N N N N 3.507 69.899 3.052 6.371 1.239 1.284 HD22 PYL 35
PYL HG22 HG22 H 0 0 N N N N N N 5.154 70.643 1.473 4.016 1.041 1.337 HG22 PYL 36
PYL HB12 HB12 H 0 0 N N N N N N 4.251 72.609 0.269 4.346 2.478 -1.350 HB12 PYL 37
PYL HB22 HB22 H 0 0 N N N N N N 2.913 71.530 0.790 2.892 2.507 -0.324 HB22 PYL 38
PYL HB32 HB32 H 0 0 N N N N N N 3.252 73.042 1.697 4.395 3.278 0.239 HB32 PYL 39
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
PYL CB2 CG2 SING N N 1
PYL CB2 HB12 SING N N 2
PYL CB2 HB22 SING N N 3
PYL CB2 HB32 SING N N 4
PYL CG2 CD2 SING N N 5
PYL CG2 CA2 SING N N 6
PYL CG2 HG22 SING N N 7
PYL CD2 CE2 SING N N 8
PYL CD2 HD32 SING N N 9
PYL CD2 HD22 SING N N 10
PYL CE2 N2 DOUB N N 11
PYL CE2 HE22 SING N N 12
PYL N2 CA2 SING N N 13
PYL CA2 C2 SING N N 14
PYL CA2 HA2 SING N N 15
PYL C2 NZ SING N N 16
PYL C2 O2 DOUB N N 17
PYL NZ CE SING N N 18
PYL NZ HZ SING N N 19
PYL CE CD SING N N 20
PYL CE HE3 SING N N 21
PYL CE HE2 SING N N 22
PYL CD CG SING N N 23
PYL CD HD3 SING N N 24
PYL CD HD2 SING N N 25
PYL CG CB SING N N 26
PYL CG HG3 SING N N 27
PYL CG HG2 SING N N 28
PYL CB CA SING N N 29
PYL CB HB3 SING N N 30
PYL CB HB2 SING N N 31
PYL CA C SING N N 32
PYL CA HA SING N N 33
PYL CA N SING N N 34
PYL C OXT SING N N 35
PYL C O DOUB N N 36
PYL OXT HXT SING N N 37
PYL N H SING N N 38
PYL N H2 SING N N 39
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
PYL SMILES ACDLabs 12.01 "O=C(NCCCCC(C(=O)O)N)C1N=CCC1C"
PYL InChI InChI 1.03 "InChI=1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9+,10-/m1/s1"
PYL InChIKey InChI 1.03 ZFOMKMMPBOQKMC-KXUCPTDWSA-N
PYL SMILES_CANONICAL CACTVS 3.385 "C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@H](N)C(O)=O"
PYL SMILES CACTVS 3.385 "C[CH]1CC=N[CH]1C(=O)NCCCC[CH](N)C(O)=O"
PYL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@@H](C(=O)O)N"
PYL SMILES "OpenEye OEToolkits" 1.7.6 "CC1CC=NC1C(=O)NCCCCC(C(=O)O)N"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
PYL "SYSTEMATIC NAME" ACDLabs 12.01 "N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine"
PYL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-6-[[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonylamino]hexanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PYL "Create component" 1999-07-08 RCSB
PYL "Modify descriptor" 2011-06-04 RCSB
PYL "Other modification" 2014-01-14 RCSB
PYL "Modify one letter code" 2014-07-17 RCSB
PYL "Other modification" 2024-02-07 PDBE
#